The bottom line is that the majority of seals in the diffs, gearbox and transfer case are lip seals, which are primarily designed to stop oil getting out.
When the diff is hot, so is the air inside it. If you rapidly cool the diff, by immersing it in water, you will also cool the air inside, which will create a low pressure zone if the breathers cannot equalise the pressure quickly.
To that end, you need to make sure that the breathers have as little restriction as possible. Obviously, if the end of the breather pipe/s is below the water the low pressure in the diff will suck water in through them, hence the reason why it is recommended that you raise the breather height if you plan on crossing deep water. If the breather pipe is blocked, that low pressure will suck water past the oil seals, no matter how high the breathers are.
So, to answer your question...
If your diffs/gearbox/transfer case breathers work well, it is less likely that you will get water where it should not be.
As I eluded to, if the breathers are working as designed, quenching a hot diff in water should not create a low enough pressure inside to suck water past the seals, but it is normally prudent to let the diff cool down a bit, just to be safe.
Use common sense to determine when it is okay to immerse them in water.